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nf-core/quantms: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[1.4.0] nfcore/quantms - [--/--/----] - Cambridge

Added

  • #423 Support for plex Correction matrices for TMT and iTRAQ analytical methods.

Changed

  • #423 Updated OpenMS==3.2.0

Fixed

Dependencies

  • openms==3.2.0

[1.3.0] nfcore/quantms - [08/04/2024] - Santiago de Cuba

Added

  • #335 (Performance improvement) Improvements in a DIA pipeline to use random/subset files for library search
  • #351 Identification workflow for DDA data
  • #362 Introduction to ms2rescore to identification workflow
  • #374 Add msgf+ database indexing step
  • #378 Introduction to ms2rescore to quant workflow
  • #386 Make validation of ontology terms optional
  • #398 Python scripts moved to quantms-utils package
  • #389 Introduction to DIANN 1.9.1 to the pipeline, only available in Singularity.
  • #396 Adds verification step to unpacking tar archives in the DECOMPRESS process
  • #397 More options included in SDRF validation.
  • #404 Add spectrum SNR features to rescore

Changed

  • #365 Updated sdrf-pipelines==0.0.29
  • #359 Updated pmultiqc==0.0.25
  • #391 Move mzML statistics to parquet files from csv
  • #386 Make optional the validation of ontology terms in the input SDRF file
  • #374 Create the common msgf+ database in one step before the msgf+ runs on each ms run file.

Fixed

  • #357 Chymotrypsin -> Chymotrypsin/P in MSGF+.
  • #355 Fixes bin/diann_convert.py
  • #316 Fixing MSGF+ error.
  • #396 Added verification of tar archive unpacking to prevent silent failures.
  • #400 The random file selection when using random_preanalysis with DIANN is now reproducible.

Dependencies

  • quantms-utils==0.0.10
  • diann==1.9.1

Parameters

  • id_only: Only perform identification, no quantification
  • min_peaks: Minimum number of peaks in a spectrum to be considered for search
  • export_decoy_psm: Export decoy PSMs
  • skip_rescoring: Skip rescoring steps
  • skip_preliminary_analysis: Skip preliminary analysis in DIA-NN
  • empirical_assembly_log: Path to the empirical assembly log file
  • random_preanalysis: Use random/subset files for library search
  • empirical_assembly_ms_n: Number of MS runs to use for empirical assembly
  • validate_ontologies: Enable or disable validating ontologies in the input SDRF file
  • skip_ms_validation: Skip validation of mass spectrometry files
  • skip_factor_validation: Skip validation of factor columns
  • skip_experimental_design_validation: Skip validation of experimental design
  • use_ols_cache_only: Use cached version of the Ontology Lookup Service
  • ms2rescore: Whether performing peptide identification rescoring with LC-MS predictors such as MS²PIP and DeepLC
  • ms2pip_model_dir: The path of ms2pip model files
  • rescore_range: Rescoring for independent run, Sample or whole experiments
  • ms2pip_model: Which deep learning model to generate feature
  • feature_generators: Which feature generator to generate feature
  • calibration_set_size: Percentage of number of calibration set for DeepLC
  • add_snr_feature_percolator: Whether add signal-to-noise ratio features for identification rescoring in percolator
  • diann_version: The version of DIA-NN used
  • random_preanalysis_seed: Set the random seed for the random selection of spectrum files to generate the empirical library

Deprecations

[1.2.0] nfcore/quantms - [11/02/2023] - Thimphu

Added

Changed

  • #314 Update for pmultiqc to pmultiqc=0.0.23
  • #308 Update for openms to openms=3.1.0
  • Update for sdrf-pipelines to sdrf-pipelines=0.0.24
  • Update for msstats to msstats=4.2.1

Fixed

Dependencies

  • New dependency on sage search engine.

Parameters

  • feature_with_id_min_score: Minimum score of a feature with a peptide identification (default: 0.10)
  • feature_without_id_min_score: Minimum score of a feature without peptide identification (transfer feature, default: 0.75)
  • lfq_intensity_threshold: Minimum intensity of a feature to be considered in the MBR algorithm (default: 1000)
  • sage_processes: Number of processes to use in SAGE search engine (default: 1)
  • diann_speclib: Path to the spectral library to use in DIA-NN (default: null)
  • convert_dotd: if convert .d file to mzml (default: false)

[1.1.1] nfcore/quantms - [03/27/23] - Berlin-Bern

Added

  • #92 Improved output docs for mzTab
  • #91 Added dev profile for nightly versions of OpenMS tools

Changed

  • #88 Updated Comet version to latest release (2023010)

Fixed

  • #93 Fixed bug in docker vs. singularity container logic in some processes.

[1.1.0] nfcore/quantms - [03/20/2023] - Berlin

  • Bugfixes and speed increases in the OpenMS tools due to version update to 2.9.1
  • Improvements in logging by adding many more process.ids
  • Large restructuring of DIA branch to increase parallelizability
  • Better error handling in MSstats step plus new parameter to filter for MSstats' adjusted p-value in the plots
  • More efficient parsing of mzML statistics in a separate step
  • A clearer distinction between per-run and experiment-wide FDRs with one parameter for each
  • More test profiles including larger "full" tests

Added

  • #176 - Add name of each ID step
  • #205 - mzTab export for DIANN outputs

Changed

  • #169 - Restruct DIA-NN step1 : Generate an in silico predicted spectral library
  • #178 - Restruct DIA-NN step2 : Preliminary analysis of individual raw files
  • #179 - Restruct DIA-NN steps 3-5 to be as parallel as possible
  • #200 - Rename MSstats/Triqler/mzTab input and output

Fixed

  • #187 - Bug fixing in proteomicsLFQ applying FDR at PSM level
  • #207 - Bug fixing in dissociation method translation for Luciphor

Dependencies

  • #203 - update openms dependency -> 3.0.0dev
  • #208 - update pmultiqc dependency -> 0.0.13. Support for DIANN in pmultiqc and enable the generation of search engine scores distributions/peptide and protein table by pmultiqc.

Parameters

  • #193 - Set the local_input_type default parameter to mzML
  • #212 - Set the min_consensus_support default parameter to 1 to filter in ConsensusID for peptides identified with both search engines
  • #200 - Add export_mztab parameter to allow to run PROTEINQUANTIFIER TMT without exporting to mzTab

[1.0] nfcore/quantms - [05/02/2022] - Havana

Initial release of nf-core/quantms, created with the nf-core template.

Added

  • New pipeline for DDA-LFQ data analysis
  • New pipeline for DDA-ISO data analysis
  • New datasets for DDA-LFQ and DDA-ISO data analysis
  • Documentation added for DDA pipeline
  • First pipeline for DIA-LFQ data analysis

Fixed

  • This is the first release - no reported issues

Dependencies

The pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency Version
thermorawfileparser 1.3.4
comet 2021010
msgf+ 2022.01.07
openms 3.1.0
sdrf-pipelines 0.0.26
percolator 3.5
pmultiqc 0.0.24
luciphor 2020_04_03
dia-nn 1.8.1
msstats 4.10.0
msstatstmt 2.10.0